Query 033697
Match_columns 113
No_of_seqs 107 out of 135
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 05:15:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033697.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033697hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3423 Transcription initiati 100.0 1.2E-37 2.6E-42 241.0 9.7 76 8-83 60-135 (176)
2 PF03540 TFIID_30kDa: Transcri 100.0 5.2E-33 1.1E-37 179.2 7.1 50 33-82 1-50 (51)
3 COG5162 Transcription initiati 100.0 7.6E-30 1.7E-34 199.4 8.8 68 16-83 70-137 (197)
4 smart00576 BTP Bromodomain tra 95.1 0.11 2.5E-06 34.3 6.2 44 38-81 10-53 (77)
5 PF07524 Bromo_TP: Bromodomain 94.3 0.23 5E-06 32.5 6.0 43 38-80 10-52 (77)
6 PF02291 TFIID-31kDa: Transcri 93.2 0.31 6.8E-06 36.2 5.9 45 38-82 16-60 (129)
7 cd07979 TAF9 TATA Binding Prot 92.9 0.49 1.1E-05 34.2 6.4 45 38-82 5-49 (117)
8 cd08045 TAF4 TATA Binding Prot 92.4 0.53 1.2E-05 36.3 6.4 46 40-85 54-99 (212)
9 PF05236 TAF4: Transcription i 91.9 0.21 4.5E-06 39.6 3.6 54 32-85 41-98 (264)
10 PF00808 CBFD_NFYB_HMF: Histon 90.5 1.5 3.1E-05 27.7 5.9 47 35-81 3-50 (65)
11 KOG1142 Transcription initiati 89.8 1.5 3.3E-05 36.5 6.9 37 48-84 169-205 (258)
12 PF03847 TFIID_20kDa: Transcri 89.4 0.91 2E-05 30.3 4.4 33 52-84 18-50 (68)
13 smart00803 TAF TATA box bindin 89.1 3.3 7.2E-05 27.2 6.9 48 34-81 2-49 (65)
14 cd07981 TAF12 TATA Binding Pro 88.3 3 6.6E-05 27.4 6.4 34 50-83 18-51 (72)
15 PLN00035 histone H4; Provision 85.4 3.6 7.9E-05 29.9 6.0 56 27-82 22-77 (103)
16 PTZ00015 histone H4; Provision 80.8 9.2 0.0002 27.7 6.5 54 29-82 25-78 (102)
17 cd00076 H4 Histone H4, one of 78.7 9.6 0.00021 26.6 5.9 54 28-81 7-60 (85)
18 PF02969 TAF: TATA box binding 78.0 13 0.00029 24.8 6.2 49 33-81 2-50 (66)
19 COG2036 HHT1 Histones H3 and H 76.4 9 0.0002 27.2 5.3 58 20-81 5-66 (91)
20 smart00417 H4 Histone H4. 76.1 14 0.00031 25.2 6.0 54 28-81 7-60 (74)
21 KOG3334 Transcription initiati 73.7 13 0.00028 29.0 5.9 45 39-83 18-62 (148)
22 cd08050 TAF6 TATA Binding Prot 64.1 29 0.00062 28.8 6.4 48 36-83 1-48 (343)
23 cd04381 RhoGap_RalBP1 RhoGap_R 56.3 32 0.00069 25.6 5.0 44 14-59 71-114 (182)
24 COG0599 Uncharacterized homolo 53.4 16 0.00035 25.6 2.9 46 19-64 15-63 (124)
25 cd04377 RhoGAP_myosin_IX RhoGA 52.7 29 0.00063 25.9 4.3 41 17-59 70-110 (186)
26 cd04374 RhoGAP_Graf RhoGAP_Gra 52.6 30 0.00064 26.7 4.4 42 17-60 89-130 (203)
27 smart00672 CAP10 Putative lipo 50.0 43 0.00094 26.8 5.1 51 29-86 190-247 (256)
28 cd04395 RhoGAP_ARHGAP21 RhoGAP 48.7 43 0.00093 25.1 4.7 43 19-63 78-120 (196)
29 PF12767 SAGA-Tad1: Transcript 47.5 52 0.0011 25.9 5.2 45 34-78 201-250 (252)
30 PF11848 DUF3368: Domain of un 44.8 29 0.00063 21.2 2.7 29 20-48 20-48 (48)
31 cd04402 RhoGAP_ARHGAP20 RhoGAP 44.4 44 0.00095 25.0 4.2 41 15-57 67-107 (192)
32 PF00123 Hormone_2: Peptide ho 44.0 22 0.00048 20.4 2.0 15 59-73 14-28 (28)
33 cd04387 RhoGAP_Bcr RhoGAP_Bcr: 43.5 45 0.00099 25.4 4.2 32 18-51 74-105 (196)
34 cd04386 RhoGAP_nadrin RhoGAP_n 43.3 54 0.0012 24.7 4.5 41 15-57 75-115 (203)
35 cd04403 RhoGAP_ARHGAP27_15_12_ 41.6 49 0.0011 24.7 4.0 40 18-59 74-113 (187)
36 cd04407 RhoGAP_myosin_IXB RhoG 41.0 57 0.0012 24.6 4.3 38 18-57 71-108 (186)
37 PF05686 Glyco_transf_90: Glyc 40.8 66 0.0014 27.2 5.1 59 29-87 259-317 (395)
38 cd04393 RhoGAP_FAM13A1a RhoGAP 39.9 1E+02 0.0022 23.0 5.5 43 14-58 72-115 (189)
39 cd04372 RhoGAP_chimaerin RhoGA 39.4 66 0.0014 24.1 4.5 40 18-59 75-114 (194)
40 cd06100 CCL_ACL-C Citryl-CoA l 38.8 54 0.0012 25.5 4.0 34 34-67 103-145 (227)
41 PF00660 SRP1_TIP1: Seripauper 38.7 27 0.00058 25.1 2.1 30 21-50 20-58 (104)
42 cd04384 RhoGAP_CdGAP RhoGAP_Cd 38.0 65 0.0014 24.5 4.2 40 16-57 74-113 (195)
43 KOG3449 60S acidic ribosomal p 38.0 40 0.00087 25.2 3.0 36 40-75 23-58 (112)
44 PRK15451 tRNA cmo(5)U34 methyl 37.7 36 0.00078 26.1 2.8 41 18-58 192-232 (247)
45 PF05931 AgrD: Staphylococcal 36.4 20 0.00044 22.8 1.1 12 32-43 33-44 (45)
46 cd04383 RhoGAP_srGAP RhoGAP_sr 35.8 80 0.0017 23.8 4.4 40 18-59 76-115 (188)
47 PF10815 ComZ: ComZ; InterPro 35.8 1E+02 0.0023 20.6 4.4 48 23-80 5-52 (56)
48 PF15374 CCDC71L: Coiled-coil 35.0 24 0.00052 31.1 1.6 26 10-35 30-57 (376)
49 cd04435 DEP_fRom2 DEP (Disheve 34.8 59 0.0013 23.2 3.3 23 52-74 45-69 (82)
50 cd06102 citrate_synt_like_2 Ci 34.0 1.8E+02 0.0038 24.0 6.5 44 22-67 154-206 (282)
51 cd04398 RhoGAP_fRGD1 RhoGAP_fR 33.7 1E+02 0.0022 22.8 4.6 42 18-61 77-118 (192)
52 cd04376 RhoGAP_ARHGAP6 RhoGAP_ 33.2 1.7E+02 0.0038 22.4 6.0 38 17-57 64-101 (206)
53 cd04375 RhoGAP_DLC1 RhoGAP_DLC 33.1 80 0.0017 24.5 4.1 43 15-59 73-115 (220)
54 PHA02517 putative transposase 32.6 73 0.0016 24.4 3.8 47 17-63 27-74 (277)
55 PF08887 GAD-like: GAD-like do 32.2 40 0.00087 24.2 2.2 22 28-50 25-46 (109)
56 cd04406 RhoGAP_myosin_IXA RhoG 32.1 1E+02 0.0022 23.2 4.4 41 18-60 71-111 (186)
57 cd04382 RhoGAP_MgcRacGAP RhoGA 32.0 95 0.0021 23.6 4.3 39 18-58 73-111 (193)
58 TIGR02425 decarb_PcaC 4-carbox 31.3 35 0.00076 24.6 1.8 46 21-66 21-70 (123)
59 KOG1488 Translational represso 31.2 1.1E+02 0.0024 27.7 5.2 55 38-93 375-434 (503)
60 cd04385 RhoGAP_ARAP RhoGAP_ARA 30.7 1.1E+02 0.0023 22.9 4.3 39 18-58 73-111 (184)
61 COG5099 RNA-binding protein of 30.4 69 0.0015 30.3 3.9 46 39-84 636-686 (777)
62 PF15127 DUF4565: Protein of u 30.2 53 0.0011 23.8 2.5 28 52-79 46-73 (91)
63 PLN02589 caffeoyl-CoA O-methyl 29.8 1.8E+02 0.004 23.2 5.8 60 1-70 1-60 (247)
64 PF08367 M16C_assoc: Peptidase 29.7 1.5E+02 0.0032 23.0 5.1 43 39-82 179-221 (248)
65 smart00070 GLUCA Glucagon like 28.5 50 0.0011 18.8 1.7 13 59-71 14-26 (27)
66 smart00546 CUE Domain that may 28.1 64 0.0014 18.7 2.2 26 23-48 4-29 (43)
67 KOG0482 DNA replication licens 27.9 88 0.0019 29.6 4.1 31 14-44 553-583 (721)
68 smart00324 RhoGAP GTPase-activ 27.6 1.5E+02 0.0032 21.0 4.4 37 18-56 60-96 (174)
69 PF10911 DUF2717: Protein of u 27.0 67 0.0015 22.7 2.5 28 21-49 5-40 (77)
70 KOG0506 Glutaminase (contains 27.0 46 0.00099 31.0 2.1 21 42-62 110-130 (622)
71 cd04404 RhoGAP-p50rhoGAP RhoGA 26.9 1.5E+02 0.0032 22.1 4.5 30 18-49 79-108 (195)
72 TIGR01527 arch_NMN_Atrans nico 24.8 1E+02 0.0022 23.3 3.4 41 15-59 123-163 (165)
73 PRK13844 recombination protein 24.4 49 0.0011 26.5 1.7 46 12-59 118-172 (200)
74 TIGR01926 peroxid_rel uncharac 24.2 2.7E+02 0.0059 19.8 6.2 49 16-67 113-161 (177)
75 TIGR00615 recR recombination p 23.6 42 0.0009 26.7 1.1 47 12-59 114-169 (195)
76 PF06073 DUF934: Bacterial pro 23.2 49 0.0011 24.1 1.3 18 32-51 56-73 (110)
77 smart00311 PWI PWI, domain in 23.2 1.4E+02 0.0031 19.4 3.4 34 38-71 27-64 (74)
78 KOG3919 Kinesin-associated fas 23.2 1.1E+02 0.0023 27.2 3.5 30 16-45 340-369 (374)
79 PF07108 PipA: PipA protein; 22.9 2.3E+02 0.0049 23.1 5.1 52 34-88 32-84 (200)
80 PF02845 CUE: CUE domain; Int 22.7 1E+02 0.0022 17.9 2.4 27 24-50 4-30 (42)
81 cd04373 RhoGAP_p190 RhoGAP_p19 22.7 1.2E+02 0.0025 22.8 3.3 40 18-59 72-111 (185)
82 PF00620 RhoGAP: RhoGAP domain 22.5 1.7E+02 0.0036 20.0 3.9 35 19-55 58-92 (151)
83 cd04391 RhoGAP_ARHGAP18 RhoGAP 22.4 2.1E+02 0.0045 21.9 4.7 38 18-57 80-117 (216)
84 PF09570 RE_SinI: SinI restric 22.2 1.1E+02 0.0024 25.4 3.2 42 32-73 74-119 (221)
85 PRK06224 citrate synthase; Pro 21.7 1.6E+02 0.0034 23.6 4.0 32 36-67 130-170 (263)
86 cd05832 Ribosomal_L12p Ribosom 21.6 2.3E+02 0.005 20.6 4.5 48 25-74 9-56 (106)
87 COG5094 TAF9 Transcription ini 21.6 2.4E+02 0.0052 22.0 4.8 39 43-82 23-62 (145)
88 PRK13916 plasmid segregation p 21.6 1.3E+02 0.0029 22.0 3.3 38 16-53 15-53 (97)
89 PF03472 Autoind_bind: Autoind 21.4 95 0.0021 20.5 2.4 26 34-60 41-66 (149)
90 PF07261 DnaB_2: Replication i 21.2 2.1E+02 0.0047 17.6 3.9 34 48-81 10-44 (77)
91 PF07967 zf-C3HC: C3HC zinc fi 20.5 70 0.0015 22.8 1.7 35 21-55 4-42 (133)
92 KOG4253 Tryptophan-rich basic 20.4 4.3E+02 0.0092 21.3 6.1 51 54-104 73-123 (175)
93 PF14706 Tnp_DNA_bind: Transpo 20.4 1.2E+02 0.0025 19.8 2.5 18 48-65 9-27 (58)
94 PHA02554 13 neck protein; Prov 20.3 1.4E+02 0.0029 25.9 3.5 43 31-80 3-45 (311)
No 1
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=100.00 E-value=1.2e-37 Score=240.99 Aligned_cols=76 Identities=46% Similarity=0.703 Sum_probs=72.3
Q ss_pred CCCCCCCCCCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 8 QQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTF 83 (113)
Q Consensus 8 ~~~~~~~~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~ 83 (113)
+.+......+|.+|+|||.+|+||+|||||+||+|||+++||+|+||||+|||||||||||||||+|||||||||-
T Consensus 60 ~~~~~~~~~~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~ 135 (176)
T KOG3423|consen 60 ANGELNPTTKDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRT 135 (176)
T ss_pred ccCCcCCCCcchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 4556677889999999999999999999999999999999999999999999999999999999999999999985
No 2
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=99.98 E-value=5.2e-33 Score=179.15 Aligned_cols=50 Identities=52% Similarity=0.895 Sum_probs=49.6
Q ss_pred CCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 33 PTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT 82 (113)
Q Consensus 33 PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r 82 (113)
|+|||+||+|||+++||+|+||||+|||||||||||+||++|||||||+|
T Consensus 1 P~IPD~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r 50 (51)
T PF03540_consen 1 PTIPDEVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIR 50 (51)
T ss_pred CCCCHHHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999998
No 3
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=99.96 E-value=7.6e-30 Score=199.41 Aligned_cols=68 Identities=40% Similarity=0.675 Sum_probs=66.5
Q ss_pred CCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 16 DDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTF 83 (113)
Q Consensus 16 ~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~ 83 (113)
.+|++|+|||++||+|+|+|||+||+|||+++||.|.|+|||||+||+|||||||||.|||||+|+|-
T Consensus 70 ~Kdktlee~l~~mDsy~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~ 137 (197)
T COG5162 70 MKDKTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQ 137 (197)
T ss_pred hhHHHHHHHHHhcccCCCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 68999999999999999999999999999999999999999999999999999999999999999985
No 4
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=95.09 E-value=0.11 Score=34.34 Aligned_cols=44 Identities=20% Similarity=0.283 Sum_probs=40.9
Q ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN 81 (113)
Q Consensus 38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~ 81 (113)
-++...|+.+||+...|...-.+.=..++|+..++..|.+||..
T Consensus 10 ~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~ 53 (77)
T smart00576 10 IAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAEL 53 (77)
T ss_pred HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999999999999999999999999999965
No 5
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=94.25 E-value=0.23 Score=32.47 Aligned_cols=43 Identities=21% Similarity=0.373 Sum_probs=39.6
Q ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYAT 80 (113)
Q Consensus 38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K 80 (113)
.++...|+.+||++..+-..-.++-.+++|+..+...+..||-
T Consensus 10 ~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae 52 (77)
T PF07524_consen 10 RSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAE 52 (77)
T ss_pred HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677889999999999999999999999999999999999984
No 6
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=93.24 E-value=0.31 Score=36.23 Aligned_cols=45 Identities=18% Similarity=0.299 Sum_probs=35.0
Q ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT 82 (113)
Q Consensus 38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r 82 (113)
.++.-.|+..|++--+|||.-.+===+.++++||..||..|+..+
T Consensus 16 ~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA 60 (129)
T PF02291_consen 16 RVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHA 60 (129)
T ss_dssp HHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 467889999999888889887666667999999999999999765
No 7
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=92.93 E-value=0.49 Score=34.16 Aligned_cols=45 Identities=18% Similarity=0.301 Sum_probs=40.8
Q ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT 82 (113)
Q Consensus 38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r 82 (113)
.++.-.|++.|.+.-+++++..+.=-+.++++||+.||..|++-.
T Consensus 5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA 49 (117)
T cd07979 5 RVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHA 49 (117)
T ss_pred HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 467889999999999999999999999999999999999999863
No 8
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=92.44 E-value=0.53 Score=36.28 Aligned_cols=46 Identities=11% Similarity=0.208 Sum_probs=40.8
Q ss_pred HHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 40 VEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFL 85 (113)
Q Consensus 40 t~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~~ 85 (113)
+..++.+.|+...|+.+..|||+|++-++.+|+.+....|+.|.-.
T Consensus 54 ~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~ 99 (212)
T cd08045 54 IRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDS 99 (212)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 4456778888888999999999999999999999999999999643
No 9
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=91.89 E-value=0.21 Score=39.56 Aligned_cols=54 Identities=15% Similarity=0.252 Sum_probs=30.4
Q ss_pred CCCCcHHHHHHHH----HhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 32 TPTIPDELVEHYL----AKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFL 85 (113)
Q Consensus 32 ~PtIPDaVt~yYL----~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~~ 85 (113)
.|.+.-.+...++ .+.|....|+-+..|||+|+|-.+.+|+.++...|+.|.-.
T Consensus 41 ~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 41 EPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp ---S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred ccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 4445444444444 44576667899999999999999999999999999999764
No 10
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=90.50 E-value=1.5 Score=27.71 Aligned_cols=47 Identities=17% Similarity=0.244 Sum_probs=34.7
Q ss_pred CcHHHHHHHHHhC-CCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 35 IPDELVEHYLAKS-GFQCPDVRLIRLVAVATQKFVAEVATDALQYATN 81 (113)
Q Consensus 35 IPDaVt~yYL~~a-Gf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~ 81 (113)
+|=+-+.-.++.. +..---..-.-+++.|++.|+..++.+|.++|+.
T Consensus 3 lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~ 50 (65)
T PF00808_consen 3 LPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQR 50 (65)
T ss_dssp S-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5777777777776 2221234456789999999999999999999985
No 11
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.79 E-value=1.5 Score=36.50 Aligned_cols=37 Identities=16% Similarity=0.141 Sum_probs=32.3
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 48 GFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFF 84 (113)
Q Consensus 48 Gf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~ 84 (113)
|=+.-|+.|..|+..-|..||+||.+-|-..||-|.-
T Consensus 169 ~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKs 205 (258)
T KOG1142|consen 169 GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKS 205 (258)
T ss_pred CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3334599999999999999999999999999998865
No 12
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=89.36 E-value=0.91 Score=30.32 Aligned_cols=33 Identities=21% Similarity=0.168 Sum_probs=28.4
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 52 PDVRLIRLVAVATQKFVAEVATDALQYATNTFF 84 (113)
Q Consensus 52 ~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~ 84 (113)
-||-+..++.--|..||.+|++.|.+.||-|.-
T Consensus 18 ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s 50 (68)
T PF03847_consen 18 LDPDVEELLLELADDFVDDVVSFACRLAKHRKS 50 (68)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 488899999999999999999999999998853
No 13
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=89.05 E-value=3.3 Score=27.16 Aligned_cols=48 Identities=17% Similarity=0.274 Sum_probs=42.2
Q ss_pred CCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 34 TIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN 81 (113)
Q Consensus 34 tIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~ 81 (113)
.+|-+-+.-..+++|.+--..-+...++=....++.+|+.||..+++-
T Consensus 2 ~~p~~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~h 49 (65)
T smart00803 2 WLPKETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRH 49 (65)
T ss_pred CCCHHHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478888899999999997666699999999999999999999988764
No 14
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=88.31 E-value=3 Score=27.45 Aligned_cols=34 Identities=24% Similarity=0.261 Sum_probs=31.2
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 50 QCPDVRLIRLVAVATQKFVAEVATDALQYATNTF 83 (113)
Q Consensus 50 ~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~ 83 (113)
..-|+-+..++.=.+..|+.+|+.+|..+||-|.
T Consensus 18 ~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~ 51 (72)
T cd07981 18 EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRK 51 (72)
T ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 5678999999999999999999999999999775
No 15
>PLN00035 histone H4; Provisional
Probab=85.44 E-value=3.6 Score=29.91 Aligned_cols=56 Identities=14% Similarity=0.180 Sum_probs=45.4
Q ss_pred hcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 27 SLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT 82 (113)
Q Consensus 27 ~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r 82 (113)
.|.|...-||-+-+.-.+.++|.+---.-+.--+.-+...|+.+|+.||..|++-.
T Consensus 22 ~~~d~i~~ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA 77 (103)
T PLN00035 22 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA 77 (103)
T ss_pred HHHhhhccCCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34567777999999999999998865444666667778899999999999998753
No 16
>PTZ00015 histone H4; Provisional
Probab=80.78 E-value=9.2 Score=27.71 Aligned_cols=54 Identities=13% Similarity=0.166 Sum_probs=45.0
Q ss_pred ccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 29 MGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT 82 (113)
Q Consensus 29 dDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r 82 (113)
-|..+-||-+-+.-.+.++|..---.-+.--+.-+...|+.+|+.||..|++-.
T Consensus 25 r~~i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA 78 (102)
T PTZ00015 25 RDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA 78 (102)
T ss_pred hhcccCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 588899999999999999999964333666667778899999999999988743
No 17
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=78.66 E-value=9.6 Score=26.60 Aligned_cols=54 Identities=15% Similarity=0.224 Sum_probs=42.2
Q ss_pred cccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN 81 (113)
Q Consensus 28 LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~ 81 (113)
|.|+..-||-+-+.-...++|..---.-+.--+.=+...|+.+|+.||..|++-
T Consensus 7 ~~~~~~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~H 60 (85)
T cd00076 7 LRDNIKGITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEH 60 (85)
T ss_pred HHHhhccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 457777899999999999999774322244555556789999999999999874
No 18
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=78.02 E-value=13 Score=24.78 Aligned_cols=49 Identities=14% Similarity=0.192 Sum_probs=37.1
Q ss_pred CCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 33 PTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN 81 (113)
Q Consensus 33 PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~ 81 (113)
+.+|-+-+.-+-+..|+..-+..+.+.++--.+--|.+|++||.++.+.
T Consensus 2 s~~~~esvk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~h 50 (66)
T PF02969_consen 2 SVFSQESVKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRH 50 (66)
T ss_dssp ----HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcCCHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678899999999999988888899999999999999999999887654
No 19
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=76.41 E-value=9 Score=27.19 Aligned_cols=58 Identities=24% Similarity=0.334 Sum_probs=46.5
Q ss_pred HHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHH----HHHHHHHHHHHHHHHHHHHHHHH
Q 033697 20 ALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIR----LVAVATQKFVAEVATDALQYATN 81 (113)
Q Consensus 20 ~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~R----LISLAAQKFISDIa~DA~Qy~K~ 81 (113)
-+.|+-.-+......||-+-++-.++++|-+ ||.. .+.=|.+-|+.+|+.||..+|+-
T Consensus 5 ~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~----Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~h 66 (91)
T COG2036 5 GLKEIRRYQRSTDLLLPKAPVRRILRKAGAE----RVSSSAIEELQEALEEYLEEIAEDAVELAEH 66 (91)
T ss_pred hHHHHHhhhhhhhhhcCchHHHHHHHHHhHH----HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556666677788999999999999999987 5543 45556778999999999999874
No 20
>smart00417 H4 Histone H4.
Probab=76.13 E-value=14 Score=25.23 Aligned_cols=54 Identities=15% Similarity=0.210 Sum_probs=41.9
Q ss_pred cccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN 81 (113)
Q Consensus 28 LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~ 81 (113)
|.|...-||-+-+.-.+.++|..---.-+.--+.=+...|+.+|+.||..|++-
T Consensus 7 ~~d~i~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~h 60 (74)
T smart00417 7 LRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEH 60 (74)
T ss_pred HHhhhcCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456677799999999999999984322244445556689999999999999864
No 21
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=73.74 E-value=13 Score=29.00 Aligned_cols=45 Identities=20% Similarity=0.284 Sum_probs=35.4
Q ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 39 LVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTF 83 (113)
Q Consensus 39 Vt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~ 83 (113)
|+.-.|+..|.+-=+|||+--+==-|.+++++|..||.-|++-.+
T Consensus 18 ~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ 62 (148)
T KOG3334|consen 18 VIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAK 62 (148)
T ss_pred HHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 566778889998777777665555678999999999999887543
No 22
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=64.09 E-value=29 Score=28.83 Aligned_cols=48 Identities=15% Similarity=0.236 Sum_probs=41.5
Q ss_pred cHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 36 PDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTF 83 (113)
Q Consensus 36 PDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~ 83 (113)
|.+-+.-+.+++|.+.-+...++.++--...++..|+++|..++|-.+
T Consensus 1 ~~~~i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hsk 48 (343)
T cd08050 1 PQESIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSK 48 (343)
T ss_pred ChhHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 345667788999999999999999999999999999999998876544
No 23
>cd04381 RhoGap_RalBP1 RhoGap_RalBP1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in RalBP1 proteins, also known as RLIP, RLIP76 or cytocentrin. RalBP1 plays an important role in endocytosis during interphase. During mitosis, RalBP1 transiently associates with the centromere and has been shown to play an essential role in the proper assembly of the mitotic apparatus. RalBP1 is an effector of the Ral GTPase which itself is an effector of Ras. RalBP1 contains a RhoGAP domain, which shows weak activity towards Rac1 and Cdc42, but not towards Ral, and a Ral effector domain binding motif. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low int
Probab=56.31 E-value=32 Score=25.63 Aligned_cols=44 Identities=20% Similarity=0.278 Sum_probs=32.0
Q ss_pred CCCCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 14 ~~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
.|.-..-|..|+..|- .|+||.++.+.+.+-++-...+.|+..+
T Consensus 71 ~h~va~lLK~fLReLP--~pLi~~~~~~~~~~~~~~~~~~~r~~~l 114 (182)
T cd04381 71 PPTVASLLKQYLRELP--EPLLTKELMPRFEEACGRPTEAEREQEL 114 (182)
T ss_pred hHHHHHHHHHHHHhCC--CccCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence 3344556788999888 5999999999998887765555555433
No 24
>COG0599 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]
Probab=53.40 E-value=16 Score=25.64 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=33.8
Q ss_pred hHHHHHHHhcccCCCCCcHHHHHHHHHhCCCC---CCChHHHHHHHHHH
Q 033697 19 AALTEFLSSLMGYTPTIPDELVEHYLAKSGFQ---CPDVRLIRLVAVAT 64 (113)
Q Consensus 19 ~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~---~~D~RI~RLISLAA 64 (113)
.....+...++++.|..||-.+.+++-..-+. .=|+|.+.||+||.
T Consensus 15 ~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~Ld~ktr~Li~ia~ 63 (124)
T COG0599 15 KVDKALAEGLEDFAPEFPELLEAFYAFGEIWFRKGALDAKTRELIAIAV 63 (124)
T ss_pred HHHHHHHhhHHHHhHhhHHHHHHHHHhhhHHhcCCCCCHHHHHHHHHHH
Confidence 45567777888999999999999444432222 24899999998874
No 25
>cd04377 RhoGAP_myosin_IX RhoGAP_myosin_IX: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in class IX myosins. Class IX myosins contain a characteristic head domain, a neck domain, a tail domain which contains a C6H2-zinc binding motif and a RhoGAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolifer
Probab=52.73 E-value=29 Score=25.86 Aligned_cols=41 Identities=24% Similarity=0.331 Sum_probs=30.7
Q ss_pred CchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 17 ~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
-..-|..|+..|- .|+||.++.+-+++.++.+..+.|+..+
T Consensus 70 va~~LK~flr~Lp--epLi~~~~~~~~~~~~~~~~~~~~i~~l 110 (186)
T cd04377 70 ITSVLKQWLRELP--EPLMTFELYENFLRAMELEEKQERVRAL 110 (186)
T ss_pred HHHHHHHHHHcCC--CccCCHHHHHHHHHHHhcCCHHHHHHHH
Confidence 3456788888887 4999999999999988766555555444
No 26
>cd04374 RhoGAP_Graf RhoGAP_Graf: GTPase-activator protein (GAP) domain for Rho-like GTPases found in GRAF (GTPase regulator associated with focal adhesion kinase); Graf is a multi-domain protein, containing SH3 and PH domains, that binds focal adhesion kinase and influences cytoskeletal changes mediated by Rho proteins. Graf exhibits GAP activity toward RhoA and Cdc42, but only weakly activates Rac1. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=52.57 E-value=30 Score=26.71 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=31.7
Q ss_pred CchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHH
Q 033697 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60 (113)
Q Consensus 17 ~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLI 60 (113)
-..-|..|+..|-+ |+||.++-+-++.-++-+..+.|+..|-
T Consensus 89 va~lLK~fLReLPe--PLi~~~~y~~~i~~~~~~~~~~ri~~l~ 130 (203)
T cd04374 89 ITSALKTYLRNLPE--PLMTYELHNDFINAAKSENLESRVNAIH 130 (203)
T ss_pred HHHHHHHHHHcCCC--CcCCHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 34567778888875 9999999999998877666666665443
No 27
>smart00672 CAP10 Putative lipopolysaccharide-modifying enzyme.
Probab=50.02 E-value=43 Score=26.77 Aligned_cols=51 Identities=16% Similarity=0.146 Sum_probs=39.3
Q ss_pred ccCCCCCcH-------HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 29 MGYTPTIPD-------ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFLR 86 (113)
Q Consensus 29 dDY~PtIPD-------aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~~~ 86 (113)
..|.|+-+| +.++++. ..+...+-|+-++|+|+.....-+-.+|-+++.|.
T Consensus 190 ~HYvPv~~d~sd~~l~~~i~~~~-------~~~~~a~~Ia~~~~~~~~~~L~~~~~~~Y~~~ll~ 247 (256)
T smart00672 190 VHYWPIKSDLSCRELKEAVDWGN-------EHDKKAQEIGKRGSEFIQQNLSMEDVYDYMFHLLQ 247 (256)
T ss_pred cceEEeeCCCchhhHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHH
Confidence 468887654 4555554 36777888889999999999998888998888764
No 28
>cd04395 RhoGAP_ARHGAP21 RhoGAP_ARHGAP21: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP21-like proteins. ArhGAP21 is a multi-domain protein, containing RhoGAP, PH and PDZ domains, and is believed to play a role in the organization of the cell-cell junction complex. It has been shown to function as a GAP of Cdc42 and RhoA, and to interact with alpha-catenin and Arf6. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=48.66 E-value=43 Score=25.11 Aligned_cols=43 Identities=23% Similarity=0.386 Sum_probs=32.0
Q ss_pred hHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHH
Q 033697 19 AALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVA 63 (113)
Q Consensus 19 ~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLA 63 (113)
.-|..|+..|- .|+||.+..+-+++.+.-+..+.|+..+-++.
T Consensus 78 ~llK~flr~Lp--~pli~~~~~~~~i~~~~~~~~~~~i~~l~~~i 120 (196)
T cd04395 78 SLLKSFFRKLP--EPLFTNELYPDFIEANRIEDPVERLKELRRLI 120 (196)
T ss_pred HHHHHHHHhCC--CccCCHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 45678888887 79999999999888776655566665555543
No 29
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=47.49 E-value=52 Score=25.90 Aligned_cols=45 Identities=16% Similarity=0.219 Sum_probs=36.6
Q ss_pred CCcHHHH-----HHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 34 TIPDELV-----EHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78 (113)
Q Consensus 34 tIPDaVt-----~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy 78 (113)
-+||.-. .-.+...|++..++..+.|+.+|.+.|+-+|+..++..
T Consensus 201 ~LPD~~~L~~Rm~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~ 250 (252)
T PF12767_consen 201 ELPDTQSLRKRMEQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLDL 250 (252)
T ss_pred cCCCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4676432 34567889988999999999999999999999987754
No 30
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=44.77 E-value=29 Score=21.17 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=22.0
Q ss_pred HHHHHHHhcccCCCCCcHHHHHHHHHhCC
Q 033697 20 ALTEFLSSLMGYTPTIPDELVEHYLAKSG 48 (113)
Q Consensus 20 ~L~eFL~~LdDY~PtIPDaVt~yYL~~aG 48 (113)
++.++++.|.+--=-||+++.+..|+++|
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L~~~g 48 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEILRRAG 48 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHHHHcC
Confidence 56777777777777788888888887776
No 31
>cd04402 RhoGAP_ARHGAP20 RhoGAP_ARHGAP20: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391 and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain, and ANXL repeats. ArhGAP20 is activated by Rap1 and induces inactivation of Rho, which in turn leads to neurite outgrowth. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=44.40 E-value=44 Score=25.04 Aligned_cols=41 Identities=12% Similarity=0.238 Sum_probs=29.3
Q ss_pred CCCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHH
Q 033697 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLI 57 (113)
Q Consensus 15 ~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~ 57 (113)
+.-..-|..|+..|- .|+||.++.+-+++-.+-...+.++.
T Consensus 67 ~~va~~lK~flreLp--epLi~~~~~~~~~~~~~~~~~~~~i~ 107 (192)
T cd04402 67 LLLASVLKDFLRNIP--GSLLSSDLYEEWMSALDQENEEEKIA 107 (192)
T ss_pred HHHHHHHHHHHHhCC--CccCCHHHHHHHHHHHccCCHHHHHH
Confidence 334456778888887 49999999998888776654344443
No 32
>PF00123 Hormone_2: Peptide hormone; InterPro: IPR000532 A number of polypeptidic hormones, mainly expressed in the intestine or the pancreas, belong to a group of structurally related peptides [, ]. Once such hormone, glucagon is widely distributed and produced in the alpha-cells of pancreatic islets []. It affects glucose metabolism in the liver [] by inhibiting glycogen synthesis, stimulating glycogenolysis and enchancing gluconeogenesis. It also increases mobilisation of glucose, free fatty acids and ketone bodies, which are metabolites produced in excess in diabetes mellitus. Glucagon is produced, like other peptide hormones, as part of a larger precursor (preproglucagon), which is cleaved to produce glucagon, glucagon-like protein I and glucagon-like protein II []. The structure of glucagon itself is fully conserved in all known mammalian species []. Other members of the structurally similar group include glicentin precursor, secretin, gastric inhibitory protein, vasoactive intestinal peptide (VIP), prealbumin, peptide HI-27 and growth hormone releasing factor.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1T5Q_A 2OBU_A 2QKH_B 2L70_A 2L71_A 2B4N_A 1GCN_A 1D0R_A 3IOL_B 2RRI_A ....
Probab=44.02 E-value=22 Score=20.38 Aligned_cols=15 Identities=27% Similarity=0.364 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHH
Q 033697 59 LVAVATQKFVAEVAT 73 (113)
Q Consensus 59 LISLAAQKFISDIa~ 73 (113)
|=.+||+|||..+.+
T Consensus 14 L~~~aak~fl~~L~~ 28 (28)
T PF00123_consen 14 LDQLAAKKFLQWLMN 28 (28)
T ss_dssp HHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHHhC
Confidence 457899999988753
No 33
>cd04387 RhoGAP_Bcr RhoGAP_Bcr: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Bcr (breakpoint cluster region protein)-like proteins. Bcr is a multidomain protein with a variety of enzymatic functions. It contains a RhoGAP and a Rho GEF domain, a Ser/Thr kinase domain, an N-terminal oligomerization domain, and a C-terminal PDZ binding domain, in addition to PH and C2 domains. Bcr is a negative regulator of: i) RacGTPase, via the Rho GAP domain, ii) the Ras-Raf-MEK-ERK pathway, via phosphorylation of the Ras binding protein AF-6, and iii) the Wnt signaling pathway through binding beta-catenin. Bcr can form a complex with beta-catenin and Tcf1. The Wnt signaling pathway is involved in cell proliferation, differentiation, and cell renewal. Bcr was discovered as a fusion partner of Abl. The Bcr-Abl fusion is characteristic for a large majority of chronic myelogenous leukemias (CML). Small GTPases cluster into distinct families, and all act as molecular switch
Probab=43.52 E-value=45 Score=25.43 Aligned_cols=32 Identities=19% Similarity=0.312 Sum_probs=25.2
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCC
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQC 51 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~ 51 (113)
..-|..|+..|-+ |+||.+..+.+.+.++.+.
T Consensus 74 a~lLK~fLReLPe--PLip~~~y~~~~~~~~~~~ 105 (196)
T cd04387 74 AGTLKLYFRELPE--PLFTDELYPNFAEGIALSD 105 (196)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHHcCC
Confidence 3467778888875 9999999999988776543
No 34
>cd04386 RhoGAP_nadrin RhoGAP_nadrin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Nadrin-like proteins. Nadrin, also named Rich-1, has been shown to be involved in the regulation of Ca2+-dependent exocytosis in neurons and recently has been implicated in tight junction maintenance in mammalian epithelium. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=43.30 E-value=54 Score=24.71 Aligned_cols=41 Identities=27% Similarity=0.362 Sum_probs=29.3
Q ss_pred CCCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHH
Q 033697 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLI 57 (113)
Q Consensus 15 ~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~ 57 (113)
|.-..-|..|+..|. .|+||.++.+-+++.+.-...+.|+.
T Consensus 75 h~va~~lK~fLreLp--~pli~~~~~~~~~~~~~~~~~~~~~~ 115 (203)
T cd04386 75 HAVASALKSYLRELP--DPLLTYNLYEDWVQAANKPDEDERLQ 115 (203)
T ss_pred HHHHHHHHHHHHhCC--CccCCHHHHHHHHHHHccCCHHHHHH
Confidence 333455777888887 49999999999998776554444543
No 35
>cd04403 RhoGAP_ARHGAP27_15_12_9 RhoGAP_ARHGAP27_15_12_9: GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP27 (also called CAMGAP1), ARHGAP15, 12 and 9-like proteins; This subgroup of ARHGAPs are multidomain proteins that contain RhoGAP, PH, SH3 and WW domains. Most members that are studied show GAP activity towards Rac1, some additionally show activity towards Cdc42. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=41.60 E-value=49 Score=24.69 Aligned_cols=40 Identities=23% Similarity=0.340 Sum_probs=29.1
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
..-|..|+..|-+ |+||.+..+.+++...-+..+.|+..+
T Consensus 74 a~lLK~fLReLPe--pLi~~~~~~~~~~~~~~~~~~~~i~~l 113 (187)
T cd04403 74 TGALKLFFRELPE--PLFPYSLFNDFVAAIKLSDYEQRVSAV 113 (187)
T ss_pred HHHHHHHHhcCCC--CcCCHHHHHHHHHHHHCCCHHHHHHHH
Confidence 3567888888875 999999999998876544444555443
No 36
>cd04407 RhoGAP_myosin_IXB RhoGAP_myosin_IXB: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXB. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolifer
Probab=40.97 E-value=57 Score=24.58 Aligned_cols=38 Identities=16% Similarity=0.209 Sum_probs=27.5
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLI 57 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~ 57 (113)
..-|..|+..|-+ |+||.++.+-++.....+..+.|+.
T Consensus 71 a~lLK~flReLPe--pLi~~~~~~~~~~~~~~~~~~~~~~ 108 (186)
T cd04407 71 TGLLKQWLRELPE--PLMTFAQYNDFLRAVELPEKQEQLQ 108 (186)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHHCCCHHHHHH
Confidence 4556778888876 9999999999888765544344443
No 37
>PF05686 Glyco_transf_90: Glycosyl transferase family 90; InterPro: IPR006598 Cryptococcus neoformans is a pathogenic fungus which most commonly affects the central nervous system and causes fatal meningoencephalitis primarily in patients with AIDS. This fungus produces a thick extracellular polysaccharide capsule which is well recognised as a virulence factor. CAP10 is required for capsule formation and virulence [].
Probab=40.83 E-value=66 Score=27.23 Aligned_cols=59 Identities=19% Similarity=0.116 Sum_probs=42.1
Q ss_pred ccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 29 MGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFLRL 87 (113)
Q Consensus 29 dDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~~~~ 87 (113)
..|.|+=++.-..-...+--+-.+++...+-|+-++|+|+.+-.+.+..+|=|++.|.=
T Consensus 259 vHYVPV~~~~d~sdL~~~v~w~~~~~~~A~~IA~~g~~f~~~~L~~~~~~~Y~~~LL~e 317 (395)
T PF05686_consen 259 VHYVPVKRDDDLSDLEEKVEWLNAHDDEAQRIAENGQRFAREYLTMEDVYCYWRRLLLE 317 (395)
T ss_pred ccEEEeccccchhhHHHHhhhcccChHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 46888766222222233333344678889999999999999999999999988887653
No 38
>cd04393 RhoGAP_FAM13A1a RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by up several orders of magnitude.
Probab=39.87 E-value=1e+02 Score=22.96 Aligned_cols=43 Identities=19% Similarity=0.026 Sum_probs=28.4
Q ss_pred CCCCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCC-CCChHHHH
Q 033697 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQ-CPDVRLIR 58 (113)
Q Consensus 14 ~~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~-~~D~RI~R 58 (113)
.|.-..-|..|+..|-+ |+||.+..+.+++-.+-. ..|.++.+
T Consensus 72 ~~~va~~lK~flr~Lp~--pLi~~~~~~~l~~~~~~~~~~~~~~~~ 115 (189)
T cd04393 72 VCSAASLLRLFLQELPE--GLIPASLQIRLMQLYQDYNGEDEFGRK 115 (189)
T ss_pred HHHHHHHHHHHHHhCCC--ccCCHHHHHHHHHHHHHccChHHHHHH
Confidence 33444567888888885 999999988887643322 34445443
No 39
>cd04372 RhoGAP_chimaerin RhoGAP_chimaerin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of chimaerins. Chimaerins are a family of phorbolester- and diacylglycerol-responsive GAPs specific for the Rho-like GTPase Rac. Chimaerins exist in two alternative splice forms that each contain a C-terminal GAP domain, and a central C1 domain which binds phorbol esters, inducing a conformational change that activates the protein; one splice form is lacking the N-terminal Src homology-2 (SH2) domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GT
Probab=39.43 E-value=66 Score=24.12 Aligned_cols=40 Identities=23% Similarity=0.353 Sum_probs=29.1
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
..-|..|+..|-+ |+||.+..+.+++-+.....|.|+..+
T Consensus 75 a~lLK~flReLP~--pLi~~~~~~~~~~~~~~~~~~~~~~~l 114 (194)
T cd04372 75 TGALKLYFRDLPI--PVITYDTYPKFIDAAKISNPDERLEAV 114 (194)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHhcCCHHHHHHHH
Confidence 3456778888875 999999999998876655555555544
No 40
>cd06100 CCL_ACL-C Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. ACL may be required for fruiting body maturation in the filamentous fungus Sordaria macrospore. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL; the first enzyme is citryl-CoA synthetase (CC
Probab=38.78 E-value=54 Score=25.46 Aligned_cols=34 Identities=35% Similarity=0.501 Sum_probs=27.0
Q ss_pred CCcHHHHHHHHHhC----CCC-----CCChHHHHHHHHHHHHH
Q 033697 34 TIPDELVEHYLAKS----GFQ-----CPDVRLIRLVAVATQKF 67 (113)
Q Consensus 34 tIPDaVt~yYL~~a----Gf~-----~~D~RI~RLISLAAQKF 67 (113)
.-++++++.++++. ||. +.|||...|.+++-+..
T Consensus 103 ~~~~~~v~~~~~~~~~ipGfGH~v~~~~DPRa~~L~~~~~~~~ 145 (227)
T cd06100 103 AAAAEFVAEYRAAKKRIPGFGHPVHKNPDPRVPRLLELARELG 145 (227)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCCCCCCchHHHHHHHHHHhc
Confidence 56778888888765 664 68999999999988753
No 41
>PF00660 SRP1_TIP1: Seripauperin and TIP1 family; InterPro: IPR000992 It has recently been shown [] that three yeast proteins, two of which are known to be induced by various stress conditions, are structurally related and are probably part of a larger family. These proteins include cold-shock inducible protein TIR1 (also known as serine-rich protein 1, SRP1), which is induced by glucose [] and cold shock []; temperature-shock inducible protein 1 (SRP2) []; seripauperins, which are closely related protein of about 13kDa (120 to 124 residues) and are generally encoded at the extremity of yeast chromosomes (eg. PAU1, PAU2, PAU3, PAU4, PAU5, PAU6, YBR301w, YGL261c, YGR294w, YHL046c, YIL176c, YIR041w and YKL224c) []; and hypothetical proteins YIL011w, YJR150c and YJR151c. These proteins all seem to start with a putative signal sequence followed by a conserved domain of about 90 residues. In TIR1, TIR2, TIP1, YIL011w, YJR150c and YJR151c, this domain is followed by a repetitive serine and alanine rich region absent in the other members of this family.; GO: 0006950 response to stress
Probab=38.74 E-value=27 Score=25.13 Aligned_cols=30 Identities=30% Similarity=0.615 Sum_probs=21.9
Q ss_pred HHHHHHhcccC-----C--C--CCcHHHHHHHHHhCCCC
Q 033697 21 LTEFLSSLMGY-----T--P--TIPDELVEHYLAKSGFQ 50 (113)
Q Consensus 21 L~eFL~~LdDY-----~--P--tIPDaVt~yYL~~aGf~ 50 (113)
++|+-..|.|| + + +||+.|.++|++-+.+.
T Consensus 20 l~Dv~snl~~Y~s~~~~~~~~~~~P~~v~~~~~~l~t~t 58 (104)
T PF00660_consen 20 LSDVKSNLNDYMSLQMTPNSGFTLPQGVLDLYMALATYT 58 (104)
T ss_pred HHHHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHHhcC
Confidence 45555666666 2 3 79999999999987654
No 42
>cd04384 RhoGAP_CdGAP RhoGAP_CdGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of CdGAP-like proteins; CdGAP contains an N-terminal RhoGAP domain and a C-terminal proline-rich region, and it is active on both Cdc42 and Rac1 but not RhoA. CdGAP is recruited to focal adhesions via the interaction with the scaffold protein actopaxin (alpha-parvin). Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=38.01 E-value=65 Score=24.45 Aligned_cols=40 Identities=15% Similarity=0.200 Sum_probs=29.3
Q ss_pred CCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHH
Q 033697 16 DDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLI 57 (113)
Q Consensus 16 ~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~ 57 (113)
.-..-|..|+..|-+ |+||.++.+.+++-.+-+..+.|+.
T Consensus 74 ~va~lLK~flReLPe--PLi~~~~y~~~~~~~~~~~~~~~~~ 113 (195)
T cd04384 74 SVSSLCKLYFRELPN--PLLTYQLYEKFSEAVSAASDEERLE 113 (195)
T ss_pred HHHHHHHHHHHhCCC--ccCCHHHHHHHHHHHhcCCHHHHHH
Confidence 334567889999986 9999999999887766544444544
No 43
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=38.00 E-value=40 Score=25.22 Aligned_cols=36 Identities=17% Similarity=0.230 Sum_probs=32.0
Q ss_pred HHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHH
Q 033697 40 VEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDA 75 (113)
Q Consensus 40 t~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA 75 (113)
+.-.|...|.+++|.||..+||.-.-|=|.|++...
T Consensus 23 ikkIl~sVG~E~d~e~i~~visel~GK~i~ElIA~G 58 (112)
T KOG3449|consen 23 IKKILESVGAEIDDERINLVLSELKGKDIEELIAAG 58 (112)
T ss_pred HHHHHHHhCcccCHHHHHHHHHHhcCCCHHHHHHHh
Confidence 566788999999999999999999999999998643
No 44
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=37.74 E-value=36 Score=26.08 Aligned_cols=41 Identities=20% Similarity=0.157 Sum_probs=30.9
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIR 58 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~R 58 (113)
..++.++...++..-+.+|.+-....|+++||...+.--+-
T Consensus 192 ~~ei~~~~~~~~~~~~~~~~~~~~~~L~~aGF~~v~~~~~~ 232 (247)
T PRK15451 192 ELEISQKRSMLENVMLTDSVETHKARLHKAGFEHSELWFQC 232 (247)
T ss_pred HHHHHHHHHHHHhhcccCCHHHHHHHHHHcCchhHHHHHHH
Confidence 45666667777777777888888999999999976654443
No 45
>PF05931 AgrD: Staphylococcal AgrD protein; InterPro: IPR009229 This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons controlled by agr [].
Probab=36.42 E-value=20 Score=22.77 Aligned_cols=12 Identities=42% Similarity=0.924 Sum_probs=10.2
Q ss_pred CCCCcHHHHHHH
Q 033697 32 TPTIPDELVEHY 43 (113)
Q Consensus 32 ~PtIPDaVt~yY 43 (113)
-|.||+|+|+-|
T Consensus 33 EpEVP~ELt~l~ 44 (45)
T PF05931_consen 33 EPEVPKELTKLY 44 (45)
T ss_pred CCcCcHHHHhhc
Confidence 589999999865
No 46
>cd04383 RhoGAP_srGAP RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an N-terminal FCH domain, a central RhoGAP domain and a C-terminal SH3 domain; this SH3 domain interacts with the intracellular proline-rich-tail of the Roundabout receptor (Robo). This interaction with Robo then activates the rhoGAP domain which in turn inhibits Cdc42 activity. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific group
Probab=35.83 E-value=80 Score=23.76 Aligned_cols=40 Identities=20% Similarity=0.397 Sum_probs=30.0
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
..-|..|+..|- .|+||.+..+.+++-++.+..+.|+..+
T Consensus 76 a~lLK~fLReLP--epLip~~~~~~~~~~~~~~~~~~~~~~l 115 (188)
T cd04383 76 AGVLKLYFRGLE--NPLFPKERFEDLMSCVKLENPTERVHQI 115 (188)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHhcCCHHHHHHHH
Confidence 446677888777 6999999999999887766555565544
No 47
>PF10815 ComZ: ComZ; InterPro: IPR024558 ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon [].
Probab=35.81 E-value=1e+02 Score=20.63 Aligned_cols=48 Identities=25% Similarity=0.431 Sum_probs=35.6
Q ss_pred HHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 23 EFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYAT 80 (113)
Q Consensus 23 eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K 80 (113)
+|++--..| +|+ ..-.|.++|.+-+=..+.-+++|- ..|.++||..-|
T Consensus 5 ~FmqIaMK~---lPE--ak~~L~k~GIeLsme~~qP~m~L~-----~~VM~eAYElG~ 52 (56)
T PF10815_consen 5 EFMQIAMKY---LPE--AKEELDKKGIELSMEMLQPLMQLL-----TKVMNEAYELGK 52 (56)
T ss_pred HHHHHHHHH---hHH--HHHHHHHcCccCCHHHHHHHHHHH-----HHHHHHHHHhhh
Confidence 344444445 455 678899999999988888888874 568999998765
No 48
>PF15374 CCDC71L: Coiled-coil domain-containing protein 71L
Probab=35.05 E-value=24 Score=31.06 Aligned_cols=26 Identities=38% Similarity=0.576 Sum_probs=20.7
Q ss_pred CCCCCCCCchHHHHHHHhcc-c-CCCCC
Q 033697 10 SSDGRHDDDAALTEFLSSLM-G-YTPTI 35 (113)
Q Consensus 10 ~~~~~~~~d~~L~eFL~~Ld-D-Y~PtI 35 (113)
++.+-.+.|.+|..||..|. | |.|+|
T Consensus 30 mS~dl~~te~qLv~Flq~Lr~eGfqP~I 57 (376)
T PF15374_consen 30 MSKDLSDTEAQLVAFLQGLRHEGFQPTI 57 (376)
T ss_pred cccccchhHHHHHHHHHHHhhcCCCcee
Confidence 34455677999999999994 3 99998
No 49
>cd04435 DEP_fRom2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) Rom2-like proteins. Rom2-like proteins share a common domain architecture, containing, beside the RhoGEF domain, a DEP, a PH (pleckstrin homology) and a CNH domain. Rom2, a yeast GEF for Rho1 and Rho2, is involved in mediating stress response via the Ras-cAMP pathway and also plays a role in mediating resistance to sphingolipid disturbances.
Probab=34.81 E-value=59 Score=23.16 Aligned_cols=23 Identities=35% Similarity=0.510 Sum_probs=19.2
Q ss_pred CChHHHHHH--HHHHHHHHHHHHHH
Q 033697 52 PDVRLIRLV--AVATQKFVAEVATD 74 (113)
Q Consensus 52 ~D~RI~RLI--SLAAQKFISDIa~D 74 (113)
+|.++.=|+ ||=||||.-||-=|
T Consensus 45 ~DRnlALllgRsLdaQkfFhdV~y~ 69 (82)
T cd04435 45 SDRNLALLLGRSLDAQKFFHDVTYD 69 (82)
T ss_pred ccHHHHHHHHHHHHHhHhhhhcccC
Confidence 899998888 57899999998543
No 50
>cd06102 citrate_synt_like_2 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and
Probab=33.97 E-value=1.8e+02 Score=24.04 Aligned_cols=44 Identities=20% Similarity=0.201 Sum_probs=30.0
Q ss_pred HHHHHhcccCCCCCcHHHHHHHHHhC----CC-----CCCChHHHHHHHHHHHHH
Q 033697 22 TEFLSSLMGYTPTIPDELVEHYLAKS----GF-----QCPDVRLIRLVAVATQKF 67 (113)
Q Consensus 22 ~eFL~~LdDY~PtIPDaVt~yYL~~a----Gf-----~~~D~RI~RLISLAAQKF 67 (113)
.+++..+.+ |.=++++++.++++. || ...|||.+.|.+++-+-+
T Consensus 154 ~~~l~e~~~--~~~~~~~v~~~l~~g~~ipGFGH~vy~~~DPRa~~L~~~~~~~~ 206 (282)
T cd06102 154 EALLDEALR--AGDAEAAVRERLRRGEALPGFGHPLYPDGDPRAAALLAALRPLG 206 (282)
T ss_pred HHHHHHhcC--CccHHHHHHHHHHcCCcccCCCCCCCCCCCccHHHHHHHHHHHh
Confidence 344444443 334467777778775 88 367999999999988754
No 51
>cd04398 RhoGAP_fRGD1 RhoGAP_fRGD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD1-like proteins. Yeast Rgd1 is a GAP protein for Rho3 and Rho4 and plays a role in low-pH response. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=33.73 E-value=1e+02 Score=22.79 Aligned_cols=42 Identities=17% Similarity=0.244 Sum_probs=28.9
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVA 61 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLIS 61 (113)
..-|..|+..|- .|+||.++.+.++..+..+.++.|+..+-.
T Consensus 77 a~~LK~fLreLp--~pLi~~~~~~~~~~~~~~~~~~~~~~~l~~ 118 (192)
T cd04398 77 ASLLKLFFRELP--EPLLTKALSREFIEAAKIEDESRRRDALHG 118 (192)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 455677888776 699999999998887655444445544433
No 52
>cd04376 RhoGAP_ARHGAP6 RhoGAP_ARHGAP6: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP6-like proteins. ArhGAP6 shows GAP activity towards RhoA, but not towards Cdc42 and Rac1. ArhGAP6 is often deleted in microphthalmia with linear skin defects syndrome (MLS); MLS is a severe X-linked developmental disorder. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=33.19 E-value=1.7e+02 Score=22.43 Aligned_cols=38 Identities=29% Similarity=0.523 Sum_probs=27.8
Q ss_pred CchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHH
Q 033697 17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLI 57 (113)
Q Consensus 17 ~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~ 57 (113)
-..-|..|+..|- .|+||.+.-+-++.-+..+ .+.|+.
T Consensus 64 va~lLK~fLReLP--ePLi~~~~y~~~i~~~~~~-~~~~~~ 101 (206)
T cd04376 64 VAALLKEFFRDMP--DPLLPRELYTAFIGTALLE-PDEQLE 101 (206)
T ss_pred HHHHHHHHHHhCC--CccCCHHHHHHHHHHHcCC-HHHHHH
Confidence 3455777888776 5999999999999877765 344443
No 53
>cd04375 RhoGAP_DLC1 RhoGAP_DLC1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of DLC1-like proteins. DLC1 shows in vitro GAP activity towards RhoA and CDC42. Beside its C-terminal GAP domain, DLC1 also contains a SAM (sterile alpha motif) and a START (StAR-related lipid transfer action) domain. DLC1 has tumor suppressor activity in cell culture. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=33.13 E-value=80 Score=24.52 Aligned_cols=43 Identities=21% Similarity=0.342 Sum_probs=30.1
Q ss_pred CCCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 15 ~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
++-...|..|+..|-+ |+||.++.+.+++-.+....+.|+..+
T Consensus 73 ~~va~lLK~flReLPe--PLlt~~l~~~fi~~~~~~~~~~~~~~l 115 (220)
T cd04375 73 YDVADMLKQYFRDLPE--PLLTNKLSETFIAIFQYVPKEQRLEAV 115 (220)
T ss_pred HHHHHHHHHHHHhCCC--ccCCHHHHHHHHHHHhcCCHHHHHHHH
Confidence 3345567788888875 999999999888765555555555433
No 54
>PHA02517 putative transposase OrfB; Reviewed
Probab=32.62 E-value=73 Score=24.42 Aligned_cols=47 Identities=15% Similarity=0.065 Sum_probs=36.2
Q ss_pred CchHHHHHHHhc-ccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHH
Q 033697 17 DDAALTEFLSSL-MGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVA 63 (113)
Q Consensus 17 ~d~~L~eFL~~L-dDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLA 63 (113)
.+.++.+++..+ .+..|...-.-+...|.+-|+..+..+|-|++.-+
T Consensus 27 ~~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~g~~vs~~tV~Rim~~~ 74 (277)
T PHA02517 27 HDDWLKSEILRVYDENHQVYGVRKVWRQLNREGIRVARCTVGRLMKEL 74 (277)
T ss_pred hhHHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCcccCHHHHHHHHHHc
Confidence 466777777766 55677777666677888889999999999988654
No 55
>PF08887 GAD-like: GAD-like domain; InterPro: IPR014983 This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain IPR004115 from INTERPRO.
Probab=32.23 E-value=40 Score=24.22 Aligned_cols=22 Identities=36% Similarity=0.721 Sum_probs=17.5
Q ss_pred cccCCCCCcHHHHHHHHHhCCCC
Q 033697 28 LMGYTPTIPDELVEHYLAKSGFQ 50 (113)
Q Consensus 28 LdDY~PtIPDaVt~yYL~~aGf~ 50 (113)
++.|...+||++++|. +.-|+.
T Consensus 25 I~kyk~~lP~~Ll~~W-~~~G~g 46 (109)
T PF08887_consen 25 IEKYKGKLPDELLEYW-KEYGFG 46 (109)
T ss_pred HHHhcCCCcHHHHHHH-HHcCCc
Confidence 4789999999999864 566765
No 56
>cd04406 RhoGAP_myosin_IXA RhoGAP_myosin_IXA: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXA. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolife
Probab=32.11 E-value=1e+02 Score=23.24 Aligned_cols=41 Identities=22% Similarity=0.330 Sum_probs=29.9
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLI 60 (113)
..-|..|+..|- .|+||.+..+-+++..|.+..+.++..+.
T Consensus 71 a~lLK~fLReLP--ePLi~~~~y~~~~~~~~~~~~~~~i~~~~ 111 (186)
T cd04406 71 ASVFKQWLRDLP--NPLMTFELYEEFLRAMGLQERRETVRGVY 111 (186)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHhcccHHHHHHHHH
Confidence 455677888887 69999999999998887655444554433
No 57
>cd04382 RhoGAP_MgcRacGAP RhoGAP_MgcRacGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in MgcRacGAP proteins. MgcRacGAP plays an important dual role in cytokinesis: i) it is part of centralspindlin-complex, together with the mitotic kinesin MKLP1, which is critical for the structure of the central spindle by promoting microtuble bundling. ii) after phosphorylation by aurora B MgcRacGAP becomes an effective regulator of RhoA and plays an important role in the assembly of the contractile ring and the initiation of cytokinesis. MgcRacGAP-like proteins contain a N-terminal C1-like domain, and a C-terminal RhoGAP domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway
Probab=32.03 E-value=95 Score=23.63 Aligned_cols=39 Identities=23% Similarity=0.262 Sum_probs=27.5
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIR 58 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~R 58 (113)
..-|..|+..|-+ |+||.+..+.+++-+.-...+.++..
T Consensus 73 aslLK~fLReLPe--PLi~~~~y~~~~~~~~~~~~~~~~~~ 111 (193)
T cd04382 73 CGCLKDFLRSLKE--PLITFALWKEFMEAAEILDEDNSRAA 111 (193)
T ss_pred HHHHHHHHHhCCC--cCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 4556778888865 99999999999887655433444433
No 58
>TIGR02425 decarb_PcaC 4-carboxymuconolactone decarboxylase. Members of this family are 4-carboxymuconolactone decarboxylase, which catalyzes the third step in the catabolism of protocatechuate (and therefore the fourth step in the catabolism of para-hydroxybenzoate, of 3-hydroxybenzoate, of vanillate, etc.). Most members of this family are encoded within protocatechuate catabolism operons. This protein is sometimes found as a fusion protein with other enzymes of the pathway, as in Rhodococcus opacus, Streptomyces avermitilis, and Caulobacter crescentus.
Probab=31.31 E-value=35 Score=24.62 Aligned_cols=46 Identities=11% Similarity=0.227 Sum_probs=33.7
Q ss_pred HHHHHHhcccCCCCCcHHHHHHH----HHhCCCCCCChHHHHHHHHHHHH
Q 033697 21 LTEFLSSLMGYTPTIPDELVEHY----LAKSGFQCPDVRLIRLVAVATQK 66 (113)
Q Consensus 21 L~eFL~~LdDY~PtIPDaVt~yY----L~~aGf~~~D~RI~RLISLAAQK 66 (113)
.......++++.|-+.+-+++|. .++.|++..+.+++-|-+|||+.
T Consensus 21 ~~~~~~~~~~~~p~~~~~~~~~~fgdv~~r~~Ld~k~R~Litla~laa~g 70 (123)
T TIGR02425 21 VDRALAATTDFDQPFQELITEYAWGTVWTRPGLTKRERSLVTIALLAALG 70 (123)
T ss_pred HHHHHhcccccCHHHHHHHHHHHhhhhhccCCCCHHHHHHHHHHHHHHCC
Confidence 33566778899998888888765 56777876777777777777764
No 59
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=31.21 E-value=1.1e+02 Score=27.71 Aligned_cols=55 Identities=18% Similarity=0.345 Sum_probs=42.1
Q ss_pred HHHHHHHHhCCCCCCChHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033697 38 ELVEHYLAKSGFQCPDVRLI-----RLVAVATQKFVAEVATDALQYATNTFFLRLLLFVFT 93 (113)
Q Consensus 38 aVt~yYL~~aGf~~~D~RI~-----RLISLAAQKFISDIa~DA~Qy~K~r~~~~~~~~~~~ 93 (113)
-|+.|.++..+. -.|.+|. .+++++.+||-|-|+..|+.|+--...-+++==+|+
T Consensus 375 YVIQHVie~g~~-~~~~~I~~~l~~~ll~~Sq~KfASnVVEk~~~~a~~~~r~~i~~Ei~~ 434 (503)
T KOG1488|consen 375 YVIQHVIEHGSP-YRDTIIIKCLLGNLLSMSQHKFASNVVEKAFLFAPPLLRALIMNEIFP 434 (503)
T ss_pred HHHHHHHhcCCh-hhhhhHHHHHHhhHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcC
Confidence 378888887777 4555554 689999999999999999999877666665544444
No 60
>cd04385 RhoGAP_ARAP RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ArfGAP activity is PIP3-dependent, ARAPs are considered integration points for phosphoinositide, Arf and Rho signaling. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=30.69 E-value=1.1e+02 Score=22.87 Aligned_cols=39 Identities=26% Similarity=0.470 Sum_probs=27.2
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIR 58 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~R 58 (113)
..-|..|+..|- .|+||.+..+.++.-+.....+.|+..
T Consensus 73 a~llK~yLreLP--~pLi~~~~~~~~~~~~~~~~~~~~i~~ 111 (184)
T cd04385 73 ADVLKRFLRDLP--DPLLTSELHAEWIEAAELENKDERIAR 111 (184)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHhCCCHHHHHHH
Confidence 345677888886 799999999999887655433444433
No 61
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=30.38 E-value=69 Score=30.30 Aligned_cols=46 Identities=28% Similarity=0.437 Sum_probs=36.7
Q ss_pred HHHHHHHhCCCCC----CChHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 39 LVEHYLAKSGFQC----PDVRLI-RLVAVATQKFVAEVATDALQYATNTFF 84 (113)
Q Consensus 39 Vt~yYL~~aGf~~----~D~RI~-RLISLAAQKFISDIa~DA~Qy~K~r~~ 84 (113)
|+.|+|...=+.- .++.+. |++.|.++||-|-|+..+..||---+.
T Consensus 636 vvq~il~~g~~~~k~~i~~~~l~~~v~elS~~kfaSnvVeK~i~~~~~~~~ 686 (777)
T COG5099 636 VVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKYASDSFK 686 (777)
T ss_pred hhhHHhhcCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchH
Confidence 7788887544432 367777 999999999999999999999866654
No 62
>PF15127 DUF4565: Protein of unknown function (DUF4565)
Probab=30.17 E-value=53 Score=23.82 Aligned_cols=28 Identities=25% Similarity=0.265 Sum_probs=22.7
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 52 PDVRLIRLVAVATQKFVAEVATDALQYA 79 (113)
Q Consensus 52 ~D~RI~RLISLAAQKFISDIa~DA~Qy~ 79 (113)
..|.+.-+|.==||+.-.||++||+|.+
T Consensus 46 ~~~~a~~vvlEyA~rLSqEIl~dAlqQW 73 (91)
T PF15127_consen 46 PSPGASPVVLEYAHRLSQEILSDALQQW 73 (91)
T ss_pred CCCCCCchhHHHHHHHHHHHHHHHHHHH
Confidence 4555566677779999999999999975
No 63
>PLN02589 caffeoyl-CoA O-methyltransferase
Probab=29.81 E-value=1.8e+02 Score=23.23 Aligned_cols=60 Identities=22% Similarity=0.198 Sum_probs=39.4
Q ss_pred CCCCCcCCCCCCCCCCCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHH
Q 033697 1 MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAE 70 (113)
Q Consensus 1 ~~~~~~~~~~~~~~~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISD 70 (113)
|.++..+||+-.+++.+-.. =.+.+++++-+|.+..+-+...|+.+..|..-|..+.+..
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~i~~Y~~~~~~~~~~~~~L~~l~~~a~~~~~~~ 60 (247)
T PLN02589 1 MANNEEQQQSQAGRHQEVGH----------KSLLQSDALYQYILETSVYPREPESMKELRELTAKHPWNI 60 (247)
T ss_pred CCCCCcccccccccccCCcc----------ccccCcHHHHHHHHHhccCCCCCHHHHHHHHHHHhcCCCC
Confidence 55555566666666543211 1446678888888777767778888888888777665443
No 64
>PF08367 M16C_assoc: Peptidase M16C associated; InterPro: IPR013578 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain appears in eukaryotes as well as bacteria and tends to be found near the C terminus of metalloproteases and related sequences belonging to MEROPS peptidase family M16 (subfamily M16C, clan ME). These include: eupitrilysin, falcilysin, PreP peptidase, CYM1 peptidase and subfamily M16C non-peptidase homologues.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 2FGE_B 3S5I_A 3S5H_A 3S5M_A 3S5K_A.
Probab=29.67 E-value=1.5e+02 Score=23.02 Aligned_cols=43 Identities=19% Similarity=0.345 Sum_probs=33.1
Q ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 39 LVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT 82 (113)
Q Consensus 39 Vt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r 82 (113)
+..-.|...-|+-.+ ||+.++.=....+-+.|+..+.+|+..|
T Consensus 179 ll~eil~~~~f~d~~-rl~~ll~~~~s~~~~~i~~~Gh~~A~~r 221 (248)
T PF08367_consen 179 LLSEILTETDFDDKE-RLKELLKELKSDMESSIISSGHSYAMSR 221 (248)
T ss_dssp HHHHHHHCB-TT-HH-HHHHHHHHHHHHHHHHHHH-HHHHHHHH
T ss_pred HHHHHHhccCCCcHH-HHHHHHHHHHHHHHHhhhhhHHHHHHHH
Confidence 445567778885444 9999999999999999999999998766
No 65
>smart00070 GLUCA Glucagon like hormones.
Probab=28.50 E-value=50 Score=18.78 Aligned_cols=13 Identities=31% Similarity=0.424 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHH
Q 033697 59 LVAVATQKFVAEV 71 (113)
Q Consensus 59 LISLAAQKFISDI 71 (113)
|=.+||+||+..+
T Consensus 14 L~~~~ar~fl~~L 26 (27)
T smart00070 14 LDQLAAKKFLQWL 26 (27)
T ss_pred HHHHHHHHHHHHh
Confidence 5578999999765
No 66
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=28.05 E-value=64 Score=18.74 Aligned_cols=26 Identities=23% Similarity=0.405 Sum_probs=20.7
Q ss_pred HHHHhcccCCCCCcHHHHHHHHHhCC
Q 033697 23 EFLSSLMGYTPTIPDELVEHYLAKSG 48 (113)
Q Consensus 23 eFL~~LdDY~PtIPDaVt~yYL~~aG 48 (113)
+-+..|.+-=|.+|++++.+.|..++
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~~~~ 29 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLEANN 29 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcC
Confidence 33455666689999999999999876
No 67
>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]
Probab=27.91 E-value=88 Score=29.62 Aligned_cols=31 Identities=16% Similarity=0.294 Sum_probs=26.0
Q ss_pred CCCCchHHHHHHHhcccCCCCCcHHHHHHHH
Q 033697 14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYL 44 (113)
Q Consensus 14 ~~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL 44 (113)
..-+-..+++.++....|.|++|+++.+|.-
T Consensus 553 epl~~~~mR~yI~~ak~~~P~vp~~l~dyi~ 583 (721)
T KOG0482|consen 553 EPLDPNLMRRYISLAKRKNPVVPEALADYIT 583 (721)
T ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHH
Confidence 3355677899999999999999999999864
No 68
>smart00324 RhoGAP GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers.
Probab=27.56 E-value=1.5e+02 Score=21.01 Aligned_cols=37 Identities=32% Similarity=0.459 Sum_probs=25.6
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRL 56 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI 56 (113)
..-|..|+..|. .|+||.+..+.++...+-...+.++
T Consensus 60 a~~lK~~Lr~Lp--~pli~~~~~~~~~~~~~~~~~~~~~ 96 (174)
T smart00324 60 AGLLKLFLRELP--EPLIPYELYEEFIEAAKVEDETERL 96 (174)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHhCCCHHHHH
Confidence 345667777665 6999999999998877643333333
No 69
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=27.03 E-value=67 Score=22.67 Aligned_cols=28 Identities=32% Similarity=0.530 Sum_probs=18.6
Q ss_pred HHHHHHhcccCCCCCcHHHHHH--------HHHhCCC
Q 033697 21 LTEFLSSLMGYTPTIPDELVEH--------YLAKSGF 49 (113)
Q Consensus 21 L~eFL~~LdDY~PtIPDaVt~y--------YL~~aGf 49 (113)
+...+..=+| .|-||+++.+| ||.++|.
T Consensus 5 I~h~l~np~D-iP~ipra~aeyLqvrfN~~yl~~sG~ 40 (77)
T PF10911_consen 5 IQHLLDNPDD-IPDIPRAAAEYLQVRFNAAYLMASGI 40 (77)
T ss_pred HHHHhcCCcc-cCCccHHHHHHHHHHhcHHHHHHhhh
Confidence 3444444333 79999999988 6666664
No 70
>KOG0506 consensus Glutaminase (contains ankyrin repeat) [Amino acid transport and metabolism]
Probab=26.96 E-value=46 Score=30.95 Aligned_cols=21 Identities=24% Similarity=0.384 Sum_probs=18.3
Q ss_pred HHHHhCCCCCCChHHHHHHHH
Q 033697 42 HYLAKSGFQCPDVRLIRLVAV 62 (113)
Q Consensus 42 yYL~~aGf~~~D~RI~RLISL 62 (113)
-.|+..|..++|||++.+++-
T Consensus 110 TALkstGLrtsDPRLk~mMd~ 130 (622)
T KOG0506|consen 110 TALKSTGLRTSDPRLKDMMDE 130 (622)
T ss_pred HHHHHcCCCcCCchHHHHHHH
Confidence 358899999999999998863
No 71
>cd04404 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=26.95 E-value=1.5e+02 Score=22.06 Aligned_cols=30 Identities=20% Similarity=0.278 Sum_probs=23.0
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCC
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGF 49 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf 49 (113)
..-|..|+..|-+ |+||.++.+..++-...
T Consensus 79 a~~LK~~lr~Lp~--pLi~~~~~~~l~~~~~~ 108 (195)
T cd04404 79 AVILKTFLRELPE--PLLTFDLYDDIVGFLNV 108 (195)
T ss_pred HHHHHHHHHhCCC--ccCCHHHHHHHHHHHcC
Confidence 4457888888885 99999988888776544
No 72
>TIGR01527 arch_NMN_Atrans nicotinamide-nucleotide adenylyltransferase. In some archaeal species, a lower-scoring paralog, uncharacterized with respect to activity, is also present. These score between trusted and noise cutoffs.
Probab=24.82 E-value=1e+02 Score=23.27 Aligned_cols=41 Identities=10% Similarity=0.149 Sum_probs=33.4
Q ss_pred CCCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 15 HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 15 ~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
.-++..+++.+..=++|.-.+|.+|.++.-+-.| +.||++|
T Consensus 123 ~~S~T~IR~~i~~~~~W~~lVP~~v~~~i~~i~~----~~r~~~~ 163 (165)
T TIGR01527 123 EYSGTEIRRRMLNGEDWEHLVPKAVADVIKEIKG----VERLRKI 163 (165)
T ss_pred cccHHHHHHHHHcCCChhhhCCHHHHHHHHHcCc----HHHHHHh
Confidence 4567899999988788999999999999988777 4566554
No 73
>PRK13844 recombination protein RecR; Provisional
Probab=24.37 E-value=49 Score=26.45 Aligned_cols=46 Identities=20% Similarity=0.426 Sum_probs=34.9
Q ss_pred CCCCCCchHHHHHHHhccc---------CCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 12 DGRHDDDAALTEFLSSLMG---------YTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 12 ~~~~~~d~~L~eFL~~LdD---------Y~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
++...++-.++++++.+++ -.||+--+.|.+|+.+. +.. +.+|.||
T Consensus 118 ~gi~p~~l~i~~L~~Ri~~~~v~EVIlAt~~t~EGe~Ta~yi~~~-lk~-~vkvtRl 172 (200)
T PRK13844 118 DGIGPSELKLDILQQIIADRKIDEVILAISPTVEGETTAHFISQM-IAK-DIKISRI 172 (200)
T ss_pred CCCChhhcCHHHHHHHHhcCCCcEEEEeCCCCccHHHHHHHHHHH-hcC-CCcEEee
Confidence 3444566677888877764 47999999999999987 555 7777776
No 74
>TIGR01926 peroxid_rel uncharacterized peroxidase-related enzyme. This protein family with length of about 200 amino acids. One member, from Myxococcus xanthus, is a selenoprotein, with an otherwise conserved Cys replaced by Sec. This family is drawn narrowly enough to suggest that These proteins contain a domain described by TIGR00778, with a CxxCxxxHxxxxxxxG motif. Some members of that family are known to act as peroxidases or correlate with resistance to oxidative stress.
Probab=24.19 E-value=2.7e+02 Score=19.83 Aligned_cols=49 Identities=16% Similarity=0.287 Sum_probs=32.4
Q ss_pred CCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHH
Q 033697 16 DDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKF 67 (113)
Q Consensus 16 ~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKF 67 (113)
..+..+-+|-..+-.=+-.|+|+..+- |.+.|| +|..|+-|+.+++..=
T Consensus 113 ~~e~a~l~~a~~~~~~~~~v~~~~~~~-l~~~g~--s~~eivel~~~i~~~~ 161 (177)
T TIGR01926 113 PRERAMLDFAVKLTATPAKVNEADFAA-LRAAGF--SDLDILDLIHSVAFFN 161 (177)
T ss_pred HHHHHHHHHHHHHhhCcccCCHHHHHH-HHHcCC--CHHHHHHHHHHHHHHH
Confidence 344555666665554334778877744 556888 6889999998887543
No 75
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.57 E-value=42 Score=26.73 Aligned_cols=47 Identities=28% Similarity=0.450 Sum_probs=34.8
Q ss_pred CCCCCCchHHHHHHHhccc---------CCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 12 DGRHDDDAALTEFLSSLMG---------YTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 12 ~~~~~~d~~L~eFL~~LdD---------Y~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
++...++-.+.++++.+++ -.||+--+.|.+||.+. +...+.+|.||
T Consensus 114 dgigp~~l~i~~L~~Ri~~~~v~EVIlAt~~tvEGe~Ta~yi~~~-lk~~~ikvtRl 169 (195)
T TIGR00615 114 DGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIARL-LQPFGVKVTRI 169 (195)
T ss_pred CCCChhhcCHHHHHHHHhcCCCcEEEEeCCCCchHHHHHHHHHHH-hhhcCCcEEee
Confidence 3444566778888888865 47999999999999986 54456676665
No 76
>PF06073 DUF934: Bacterial protein of unknown function (DUF934); InterPro: IPR008318 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.24 E-value=49 Score=24.13 Aligned_cols=18 Identities=33% Similarity=0.722 Sum_probs=15.1
Q ss_pred CCCCcHHHHHHHHHhCCCCC
Q 033697 32 TPTIPDELVEHYLAKSGFQC 51 (113)
Q Consensus 32 ~PtIPDaVt~yYL~~aGf~~ 51 (113)
-.++||.+ .||.++||+.
T Consensus 56 Gdvl~DQl--~~l~R~GFds 73 (110)
T PF06073_consen 56 GDVLRDQL--FYLRRCGFDS 73 (110)
T ss_pred ccchHHHH--HHHHHcCCCE
Confidence 46788887 5999999996
No 77
>smart00311 PWI PWI, domain in splicing factors.
Probab=23.23 E-value=1.4e+02 Score=19.45 Aligned_cols=34 Identities=24% Similarity=0.450 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCC-CCChHHHHHHHH---HHHHHHHHH
Q 033697 38 ELVEHYLAKSGFQ-CPDVRLIRLVAV---ATQKFVAEV 71 (113)
Q Consensus 38 aVt~yYL~~aGf~-~~D~RI~RLISL---AAQKFISDI 71 (113)
.|++|.+....=. .+|+.+.+|... .|.+|+.++
T Consensus 27 ~vvd~i~~~l~~~~~~~~l~~~L~~~~f~da~~Fv~~L 64 (74)
T smart00311 27 TLVEFILSQIRQHKGPQAKLLQINLTGFEDAEEFVDKL 64 (74)
T ss_pred HHHHHHHHHHHhCCChHHHHHHHHhhcchhHHHHHHHH
Confidence 3455544443322 578888888665 577777665
No 78
>KOG3919 consensus Kinesin-associated fasciculation and elongation protein involved in axonal transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.22 E-value=1.1e+02 Score=27.16 Aligned_cols=30 Identities=23% Similarity=0.342 Sum_probs=26.6
Q ss_pred CCchHHHHHHHhcccCCCCCcHHHHHHHHH
Q 033697 16 DDDAALTEFLSSLMGYTPTIPDELVEHYLA 45 (113)
Q Consensus 16 ~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~ 45 (113)
.+-+-|-..|..|.+=.|++|-=+|+|+|+
T Consensus 340 ~~lq~LtkiL~Am~eds~~VPtLLTDYILk 369 (374)
T KOG3919|consen 340 EDLQILTKILRAMKEDSEKVPSLLTDYILK 369 (374)
T ss_pred hhHHHHHHHHHHhhCCcccccHHHHHHHHH
Confidence 445678899999999999999999999997
No 79
>PF07108 PipA: PipA protein; InterPro: IPR010777 This family consists of several Salmonella PipA (pathogenicity island-encoded protein A) and related phage sequences. PipA is thought to contribute to enteric but not to systemic salmonellosis [].
Probab=22.93 E-value=2.3e+02 Score=23.07 Aligned_cols=52 Identities=17% Similarity=0.270 Sum_probs=34.4
Q ss_pred CCcHHHHHHHHHhC-CCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 34 TIPDELVEHYLAKS-GFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFLRLL 88 (113)
Q Consensus 34 tIPDaVt~yYL~~a-Gf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~~~~~ 88 (113)
+=|..+++|++.-+ |.++ |..|--=+=--+.+=+|.|.++||..+-+ |.||.
T Consensus 32 L~Pe~~~ey~iSg~ggidp-d~EiDdd~Y~eC~~eLS~il~~AYtqs~T--FRRLm 84 (200)
T PF07108_consen 32 LEPEQVVEYLISGAGGIDP-DTEIDDDIYDECYDELSSILQNAYTQSET--FRRLM 84 (200)
T ss_pred cCHHHHHHHHHhCCCCCCC-cccccchHHHHHHHHHHHHHHHHHhhhHH--HHHHH
Confidence 45799999999984 5533 33332223334678889999999987765 44444
No 80
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=22.75 E-value=1e+02 Score=17.89 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=21.3
Q ss_pred HHHhcccCCCCCcHHHHHHHHHhCCCC
Q 033697 24 FLSSLMGYTPTIPDELVEHYLAKSGFQ 50 (113)
Q Consensus 24 FL~~LdDY~PtIPDaVt~yYL~~aGf~ 50 (113)
-+.+|.+--|-++.+++...|.+++.+
T Consensus 4 ~v~~L~~mFP~~~~~~I~~~L~~~~~~ 30 (42)
T PF02845_consen 4 MVQQLQEMFPDLDREVIEAVLQANNGD 30 (42)
T ss_dssp HHHHHHHHSSSS-HHHHHHHHHHTTTT
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCC
Confidence 345667778999999999999888765
No 81
>cd04373 RhoGAP_p190 RhoGAP_p190: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p190-like proteins. p190, also named RhoGAP5, plays a role in neuritogenesis and axon branch stability. p190 shows a preference for Rho, over Rac and Cdc42, and consists of an N-terminal GTPase domain and a C-terminal GAP domain. The central portion of p190 contains important regulatory phosphorylation sites. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=22.67 E-value=1.2e+02 Score=22.75 Aligned_cols=40 Identities=28% Similarity=0.365 Sum_probs=27.7
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRL 59 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RL 59 (113)
..-|..||..|- .|+||-++.+.++.-+|-+....|+..+
T Consensus 72 a~~lK~fLreLP--ePlip~~~~~~~~~~~~~~~~~~~i~~l 111 (185)
T cd04373 72 AGALKSFFSELP--DPLIPYSMHLELVEAAKINDREQRLHAL 111 (185)
T ss_pred HHHHHHHHhcCC--chhccHHHHHHHHHHHhCCCHHHHHHHH
Confidence 345677777776 7999999999888877744444454433
No 82
>PF00620 RhoGAP: RhoGAP domain; InterPro: IPR000198 Members of the Rho family of small G proteins transduce signals from plasma-membrane receptors and control cell adhesion, motility and shape by actin cytoskeleton formation. Like all other GTPases, Rho proteins act as molecular switches, with an active GTP-bound form and an inactive GDP-bound form. The active conformation is promoted by guanine-nucleotide exchange factors, and the inactive state by GTPase-activating proteins (GAPs) which stimulate the intrinsic GTPase activity of small G proteins. This entry is a Rho/Rac/Cdc42-like GAP domain, that is found in a wide variety of large, multi-functional proteins []. A number of structure are known for this family [, , ]. The domain is composed of seven alpha helices. This domain is also known as the breakpoint cluster region-homology (BH) domain.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1RGP_A 1AM4_B 1GRN_B 2NGR_B 1OW3_A 1TX4_A 3BYI_B 1XA6_A 3FK2_B 1F7C_A ....
Probab=22.55 E-value=1.7e+02 Score=20.00 Aligned_cols=35 Identities=31% Similarity=0.493 Sum_probs=23.4
Q ss_pred hHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChH
Q 033697 19 AALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVR 55 (113)
Q Consensus 19 ~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~R 55 (113)
.-|..||..|. .|+||+++.+-+++...-...+.+
T Consensus 58 ~~lK~~L~~lp--~pli~~~~~~~~~~~~~~~~~~~~ 92 (151)
T PF00620_consen 58 SLLKRFLRELP--EPLIPSELYDKFIAASKSADEEEQ 92 (151)
T ss_dssp HHHHHHHHHSS--STSTTHHHHHHHHHHHTSSSHHHH
T ss_pred ccceeeeeccc--cchhhhhHHHHHhhhhccchhhHH
Confidence 34566777775 589999998888865444443333
No 83
>cd04391 RhoGAP_ARHGAP18 RhoGAP_ARHGAP18: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP18-like proteins. The function of ArhGAP18 is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=22.43 E-value=2.1e+02 Score=21.89 Aligned_cols=38 Identities=18% Similarity=0.321 Sum_probs=27.2
Q ss_pred chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHH
Q 033697 18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLI 57 (113)
Q Consensus 18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~ 57 (113)
..-|..|+..|- .|+||.+..+.+++-.+.+..+.++.
T Consensus 80 a~lLK~flReLP--ePLi~~~~~~~~~~~~~~~~~~~~~~ 117 (216)
T cd04391 80 ASLLKLFIRELP--QPLLTVEYLPAFYSVQGLPSKKDQLQ 117 (216)
T ss_pred HHHHHHHHHhCC--CccCCHHHHHHHHHHHcCCCHHHHHH
Confidence 445666777775 69999999999988777655444443
No 84
>PF09570 RE_SinI: SinI restriction endonuclease; InterPro: IPR019070 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the restriction endonuclease SinI, which recognises and cleaves the double-stranded sequence G^GWCC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=22.21 E-value=1.1e+02 Score=25.36 Aligned_cols=42 Identities=21% Similarity=0.374 Sum_probs=31.7
Q ss_pred CCCCcHHHHHHHHHhC-CCCC---CChHHHHHHHHHHHHHHHHHHH
Q 033697 32 TPTIPDELVEHYLAKS-GFQC---PDVRLIRLVAVATQKFVAEVAT 73 (113)
Q Consensus 32 ~PtIPDaVt~yYL~~a-Gf~~---~D~RI~RLISLAAQKFISDIa~ 73 (113)
+-||||++++-.|+.+ |+.. ...+....+|.||..-+-++..
T Consensus 74 p~TvpDE~vs~i~~~~~~~s~e~l~~i~~~HrlsM~aENivG~LLE 119 (221)
T PF09570_consen 74 PTTVPDEMVSVIMNASFGYSQEDLELIKEGHRLSMAAENIVGALLE 119 (221)
T ss_pred CCCCChHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999999954 5543 3455566789999888888775
No 85
>PRK06224 citrate synthase; Provisional
Probab=21.71 E-value=1.6e+02 Score=23.58 Aligned_cols=32 Identities=34% Similarity=0.408 Sum_probs=23.8
Q ss_pred cHHHHHHHHHhC----CCC-----CCChHHHHHHHHHHHHH
Q 033697 36 PDELVEHYLAKS----GFQ-----CPDVRLIRLVAVATQKF 67 (113)
Q Consensus 36 PDaVt~yYL~~a----Gf~-----~~D~RI~RLISLAAQKF 67 (113)
++++++-++++. ||. +.|||...|.+++-+-.
T Consensus 130 ~~~~v~~~~~~~~~ipGFGH~~y~~~DPRa~~L~~~~~~~~ 170 (263)
T PRK06224 130 ARAIVAEYRAAGKRVPGFGHPLHKPVDPRAPRLLALAREAG 170 (263)
T ss_pred HHHHHHHHHHcCCCcCCCCCCCCCCCCchHHHHHHHHHHhc
Confidence 445667777763 774 57999999999987754
No 86
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=21.62 E-value=2.3e+02 Score=20.62 Aligned_cols=48 Identities=23% Similarity=0.321 Sum_probs=37.0
Q ss_pred HHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHH
Q 033697 25 LSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATD 74 (113)
Q Consensus 25 L~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~D 74 (113)
|..+..- .|=.+-+...|..+|.++.+-+++-|++.-.-|=|.|++..
T Consensus 9 LL~~~G~--eITae~I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa~ 56 (106)
T cd05832 9 LLHYAGK--EINEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKK 56 (106)
T ss_pred HHHhcCC--CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHh
Confidence 3344444 45577888999999999999999999988877777777654
No 87
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=21.62 E-value=2.4e+02 Score=21.98 Aligned_cols=39 Identities=26% Similarity=0.431 Sum_probs=24.5
Q ss_pred HHHhCCCC-CCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 43 YLAKSGFQ-CPDVRLIRLVAVATQKFVAEVATDALQYATNT 82 (113)
Q Consensus 43 YL~~aGf~-~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r 82 (113)
.|..-|.+ |+|.-...|+-. |+++-.|+..||+-|+|-.
T Consensus 23 iL~Slgi~~ye~~VplQLl~F-AhRYTq~vl~Dalvya~ht 62 (145)
T COG5094 23 ILRSLGIEEYEPKVPLQLLEF-AHRYTQDVLEDALVYAKHT 62 (145)
T ss_pred HHHhcCchhhCccchHHHHHH-HHHHHHHHHHHHHHHHHhc
Confidence 33444443 233333344443 5889999999999999865
No 88
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=21.60 E-value=1.3e+02 Score=21.99 Aligned_cols=38 Identities=18% Similarity=0.279 Sum_probs=30.7
Q ss_pred CCchHHHHHHHhccc-CCCCCcHHHHHHHHHhCCCCCCC
Q 033697 16 DDDAALTEFLSSLMG-YTPTIPDELVEHYLAKSGFQCPD 53 (113)
Q Consensus 16 ~~d~~L~eFL~~LdD-Y~PtIPDaVt~yYL~~aGf~~~D 53 (113)
.+-.+|=|||.++-+ -.|+-=-+|.+-|.+..||.++=
T Consensus 15 ~~~~~iF~FL~~~P~GT~~~~iR~~L~rYI~~~G~~~Pi 53 (97)
T PRK13916 15 EDYPQIFDFLENVPRGTKTAHIREALRRYIEEIGENPPI 53 (97)
T ss_pred cccHHHHHHHHHCCCCCccHHHHHHHHHHHHhcCCCCCC
Confidence 345789999999965 46777788899999999999753
No 89
>PF03472 Autoind_bind: Autoinducer binding domain; InterPro: IPR005143 This domain binds N-acyl homoserine lactones (AHLs), which are also known as autoinducers. These are small, diffusible molecules used as communication signals in a large variety of proteobacteria. It is almost always found in association with the DNA-binding LuxR domain (IPR000792 from INTERPRO). The autoinducer binding domain forms the N-terminal region of the protein, while the DNA-binding domain forms the C-terminal region. In most cases, binding of AHL by this N-terminal domain leads to unmasking of the DNA-binding domain, allowing it to bind DNA and activate transcription []. In rare cases, some LuxR proteins such as EsaR, act as repressors []. In these proteins binding of AHL to this domain leads to inactivation of the protein as a transcriptional regulator. A large number of processes have been shown to be regulated by LuxR proteins, including bioluminescence, production of virulence factors in plant and animal pathogens, antibiotic production and plasmid transfer. Structural studies of TraR from Agrobacterium tumefaciens [, ] show that the functional protein is a homodimer. Binding of the cognate AHL is required for protein folding, resistance to proteases and dimerisation. The autoinducer binding domain binds its cognate AHL in an alpha/beta/alpha sandwich and provides an extensive dimerisation surface, though residues from the C-terminal region also make some contribution to dimerisation. The autoinducer binding domain is also required for interaction with RpoA, allowing transcription to occur []. There are some proteins which consist solely of the autoinducer binding domain. The function of these is not known, but TrlR from Agrobacterium has been shown to inhibit the activity of TraR by the formation of inactive heterodimers [].; PDB: 3SZT_A 1H0M_A 1L3L_B 2Q0O_B 2UV0_F 3IX8_A 3IX4_C 3IX3_A 3JPU_D 3QP8_A ....
Probab=21.42 E-value=95 Score=20.50 Aligned_cols=26 Identities=31% Similarity=0.464 Sum_probs=19.5
Q ss_pred CCcHHHHHHHHHhCCCCCCChHHHHHH
Q 033697 34 TIPDELVEHYLAKSGFQCPDVRLIRLV 60 (113)
Q Consensus 34 tIPDaVt~yYL~~aGf~~~D~RI~RLI 60 (113)
..|++..++|.++ |+.-.||-+.++.
T Consensus 41 ~~p~~w~~~Y~~~-~~~~~DPv~~~~~ 66 (149)
T PF03472_consen 41 NYPDEWLEHYEER-GYFRIDPVVRHAR 66 (149)
T ss_dssp SS-HHHHHHHHHT-TGGGT-HHHHHHC
T ss_pred cCCHHHHHHHHHc-CCcCCCHHHHHHH
Confidence 6799999999988 6667788877665
No 90
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=21.23 E-value=2.1e+02 Score=17.58 Aligned_cols=34 Identities=24% Similarity=0.329 Sum_probs=23.4
Q ss_pred CCCCCChHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Q 033697 48 GFQCPDVRLIRLVAVATQ-KFVAEVATDALQYATN 81 (113)
Q Consensus 48 Gf~~~D~RI~RLISLAAQ-KFISDIa~DA~Qy~K~ 81 (113)
|-..+..-...|-.+... .|=.|++..|++||..
T Consensus 10 ~~~~s~~e~~~l~~~~~~~~~~~~~v~~ai~~~~~ 44 (77)
T PF07261_consen 10 GRPPSPSEIEKLEKWIDDYGFSPEVVNEAIEYALE 44 (77)
T ss_dssp TSS--HHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 555555555556565554 8999999999999985
No 91
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=20.55 E-value=70 Score=22.81 Aligned_cols=35 Identities=23% Similarity=0.330 Sum_probs=30.2
Q ss_pred HHHHHHhcccCCCC----CcHHHHHHHHHhCCCCCCChH
Q 033697 21 LTEFLSSLMGYTPT----IPDELVEHYLAKSGFQCPDVR 55 (113)
Q Consensus 21 L~eFL~~LdDY~Pt----IPDaVt~yYL~~aGf~~~D~R 55 (113)
-++|+..|+-|.+. =|+.|...-+++-|..|.|+.
T Consensus 4 r~~~l~RL~Tf~~~~W~~kp~~lspl~cA~~GW~~~~~d 42 (133)
T PF07967_consen 4 REDFLRRLETFKSLTWFPKPPWLSPLECARRGWICVSKD 42 (133)
T ss_pred HHHHHHHHHHcccccccCCCcccCHHHHHHcCCCcCCCC
Confidence 57899999999874 599999999999999987743
No 92
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=20.42 E-value=4.3e+02 Score=21.25 Aligned_cols=51 Identities=14% Similarity=0.197 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccceeecC
Q 033697 54 VRLIRLVAVATQKFVAEVATDALQYATNTFFLRLLLFVFTRFQGFSLFTNS 104 (113)
Q Consensus 54 ~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~~~~~~~~~~~~~~~~~~~~~ 104 (113)
.|+-|=+.=-.||.=....+.+.|.+..++.|.+.+||+++--+++.++--
T Consensus 73 aRlnRKi~kl~~ele~qs~n~~~q~~~~K~vlSv~f~vl~~~~~~~~~~K~ 123 (175)
T KOG4253|consen 73 ARLNRKINKLDKELETQSKNKTAQAHLHKWVLSVAFYVLKIMYGKTPVYKL 123 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhceeeee
Confidence 477777888889999999999999999999999999999999888887653
No 93
>PF14706 Tnp_DNA_bind: Transposase DNA-binding; PDB: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A.
Probab=20.39 E-value=1.2e+02 Score=19.84 Aligned_cols=18 Identities=39% Similarity=0.394 Sum_probs=11.8
Q ss_pred CCCCCChHH-HHHHHHHHH
Q 033697 48 GFQCPDVRL-IRLVAVATQ 65 (113)
Q Consensus 48 Gf~~~D~RI-~RLISLAAQ 65 (113)
+.+-.|+|+ +||++|+.+
T Consensus 9 ~~~lGD~Rl~~Rl~~l~~~ 27 (58)
T PF14706_consen 9 SADLGDKRLTRRLVKLAES 27 (58)
T ss_dssp T--SSSHHHHHHHHHHHHH
T ss_pred cCCcCcchHHHHHHHHHHH
Confidence 444569988 788888753
No 94
>PHA02554 13 neck protein; Provisional
Probab=20.31 E-value=1.4e+02 Score=25.90 Aligned_cols=43 Identities=23% Similarity=0.351 Sum_probs=32.4
Q ss_pred CCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697 31 YTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYAT 80 (113)
Q Consensus 31 Y~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K 80 (113)
|.|.=|-++.+|+|+|-|.+.-+..|. .-=|.|.+.+|+|+-.
T Consensus 3 ~~~~sp~eLkD~iLRrLGAPii~Ievt-------~dQi~D~I~rALely~ 45 (311)
T PHA02554 3 YNPNNPRELKDYILRRLGAPIINVEVT-------EDQIYDCIQRALELYG 45 (311)
T ss_pred CCCCCHHHHHHHHHHhcCCCeeEeecC-------HHHHHHHHHHHHHHHH
Confidence 578889999999999999986544432 3346778888877644
Done!